Well you can have a skill based system without having it be the end-all-be-all, specially in a game like this. You can award skill points over time which can be used to unlock the ability to use upgraded weapons/vehicles, etc. Kinda like the unlockables in games like the Battlefield series, etc.
In one way you're right, you would have more players initially probably, but like most FPSes that have been released, there's a huge spike after release then it dies out over time. That's great for console/PC FPS games, their business model is based on initial box sales. MMO's rely on subscriptions, keeping players around for longer periods of time. With most players, you have to give them something to invest in, a reason to stick around, etc.
All that being said though, just having the GTA name on the box is going to sell it at this point regardless.